[BioC] Defining Weights in marrayNorm.
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Wed Aug 13 13:22:52 MEST 2003
Almost finished with this thread, thanks alot for your help :-)
>From the documentation on maNormMain and maNormLoess, I should be able to use something like this to get my weights considered:
mydata.norm <- maNormMain(mydata, f.loc = list(maNormLoess(x="maA",y="maM",z=NULL, w=weights)))
where weights is my vector of weights. However, if I try that, I get:
Error in model.frame(formula, rownames, variables, varnames, extras, extranames, :
invalid variable type
The documentation states that w should be:
w: An optional numeric vector of weights.
I have weights as a vector, 19200 long, all ones and zeros. My marrayRaw objects have 19200 spots. So I do wonder what could be going wrong, I am sure it is me doing something wrong rather than a bug, however the documentation doesn't really give many clues away :-(
Finally, if I try (without the weights):
mydata.norm <- maNormMain(mydata, f.loc = list(maNormLoess(x="maA",y="maM",z=NULL)))
I get no errors, so it is the weights that are causing the problems!
Sorry to go on about this, I know I should use limma but I really would like to get this working!
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